def test_supercell():
from numpy import array, all, abs
from pylada.dftcrystal import Supercell, Crystal
from pylada.error import ValueError
structure = Crystal(136, 4.63909875, 2.97938395, \
ifhr=0, \
shift=0)\
.add_atom(0, 0, 0, 'Ti')\
.add_atom(0.306153, 0.306153, 0, 'O') \
.append(Supercell([[2,0,0],[0,1,0],[0,0,1]]))
assert len(structure.eval()) == 2 * 6
structure[-1].matrix[2,2] = 2
assert len(structure.eval()) == 2 * 2 * 6
map = structure[-1].output_map()
assert 'supercel' in map
a = Supercell()
a.read_input(map['supercel'])
assert all(abs(a.matrix - structure[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Supercell': Supercell}).matrix - a.matrix) < 1e-8)
# test errors
try: structure[-1].matrix = array( [[0]*3]*3 )
except ValueError: pass
else: raise Exception()
structure[-1].matrix = array([[1,0],[0,1]])
try: structure.print_input()
except ValueError: pass
else: raise Exception()
map = structure[-1].output_map()
assert 'supercel' in map
a = Supercell()
a.read_input(map['supercel'])
assert all(abs(a.matrix - structure[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Supercell': Supercell}).matrix - a.matrix) < 1e-8)
def test_elastic():
""" Test elastic keyword. """
from pickle import loads, dumps
from numpy import array, all, abs, identity, dot
from pylada.dftcrystal import Crystal, Elastic
epsilon = array([[0, 0, 0], [0, 0, 0], [0, 0, 0.1]])
crystal = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, 'Si')
structure = crystal.eval()
crystal.append(Elastic([[0, 0, 0], [0, 0, 0], [0, 0, 0.1]]))
assert all(abs(dot(identity(3) + epsilon, structure.cell) - crystal.eval().cell) < 1e-8)
assert all(abs(crystal.eval()[0].pos - dot(identity(3) + epsilon, structure[0].pos)) < 1e-8)
assert all(abs(crystal.eval()[1].pos - dot(identity(3) + epsilon, structure[1].pos)) < 1e-8)
assert abs(crystal.eval()[0].pos[1] - crystal.eval()[0].pos[0]) < 1e-8
assert abs(crystal.eval()[1].pos[2] / crystal.eval()[1].pos[1] - 1.1) < 1e-8
assert abs(crystal.eval()[1].pos[1] - crystal.eval()[1].pos[0]) < 1e-8
a = Elastic()
a.raw = crystal[-1].raw
assert a.is_epsilon == crystal[-1].is_epsilon
assert all(abs(a.matrix - crystal[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Elastic': Elastic}).matrix - a.matrix) < 1e-8)
assert eval(repr(a), {'Elastic': Elastic}).is_epsilon == a.is_epsilon
assert loads(dumps(a)).is_epsilon == a.is_epsilon
assert all(abs(loads(dumps(a)).matrix - a.matrix) < 1e-8)
z = dot(epsilon, structure.cell)
crystal[-1].matrix = z
crystal[-1].is_epsilon = False
assert all(abs(dot(identity(3) + epsilon, structure.cell) - crystal.eval().cell) < 1e-8)
assert all(abs(crystal.eval()[0].pos - dot(identity(3) + epsilon, structure[0].pos)) < 1e-8)
assert all(abs(crystal.eval()[1].pos - dot(identity(3) + epsilon, structure[1].pos)) < 1e-8)
a = Elastic()
a.raw = crystal[-1].raw
assert a.is_epsilon == crystal[-1].is_epsilon
assert all(abs(a.matrix - crystal[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Elastic': Elastic}).matrix - a.matrix) < 1e-8)
assert eval(repr(a), {'Elastic': Elastic}).is_epsilon == a.is_epsilon
assert loads(dumps(a)).is_epsilon == a.is_epsilon
assert all(abs(loads(dumps(a)).matrix - a.matrix) < 1e-8)
epsilon = array([[0, 0, 0], [0, 0, 0], [0, 0.1, 0]])
crystal[-1].matrix = epsilon
crystal[-1].is_epsilon = True
assert all(abs(dot(identity(3) + epsilon, structure.cell) - crystal.eval().cell) < 1e-8)
assert all(abs(crystal.eval()[0].pos - dot(identity(3) + epsilon, structure[0].pos)) < 1e-8)
assert all(abs(crystal.eval()[1].pos - dot(identity(3) + epsilon, structure[1].pos)) < 1e-8)
a = Elastic()
a.raw = crystal[-1].raw
assert a.is_epsilon == crystal[-1].is_epsilon
assert all(abs(a.matrix - crystal[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Elastic': Elastic}).matrix - a.matrix) < 1e-8)
assert eval(repr(a), {'Elastic': Elastic}).is_epsilon == a.is_epsilon
assert loads(dumps(a)).is_epsilon == a.is_epsilon
assert all(abs(loads(dumps(a)).matrix - a.matrix) < 1e-8)
z = dot(epsilon, structure.cell)
crystal[-1].matrix = z
crystal[-1].is_epsilon = False
assert all(abs(dot(identity(3) + epsilon, structure.cell) - crystal.eval().cell) < 1e-8)
assert all(abs(crystal.eval()[0].pos - dot(identity(3) + epsilon, structure[0].pos)) < 1e-8)
assert all(abs(crystal.eval()[1].pos - dot(identity(3) + epsilon, structure[1].pos)) < 1e-8)
a = Elastic()
a.raw = crystal[-1].raw
assert a.is_epsilon == crystal[-1].is_epsilon
assert all(abs(a.matrix - crystal[-1].matrix) < 1e-8)
assert all(abs(eval(repr(a), {'Elastic': Elastic}).matrix - a.matrix) < 1e-8)
assert eval(repr(a), {'Elastic': Elastic}).is_epsilon == a.is_epsilon
assert loads(dumps(a)).is_epsilon == a.is_epsilon
assert all(abs(loads(dumps(a)).matrix - a.matrix) < 1e-8)